# HG changeset patch # User trinity_ctat # Date 1531842748 14400 # Node ID 966ea55e1aaee60a14224faba8a68189fb959d93 Upload ctat tools. diff -r 000000000000 -r 966ea55e1aae ctat_gmap_fusion.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_gmap_fusion.xml Tue Jul 17 11:52:28 2018 -0400 @@ -0,0 +1,55 @@ + + Fusion-finding Using De novo RNA-Seq Transcript Assemblies + + gmap-fusion + + + GMAP-fusion + -T $assembled_trans + --left_fq $left_input + --right_fq $right_input + --genome_lib_dir "${genome_resource_lib.fields.path}" + --output "subdir" + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +GMAP-fusion is a utility for identifying candidate fusion transcripts based on transcript sequences reconstructed via RNA-Seq de novo transcriptome assembly. Please read more here_. + +.. _here: https://github.com/GMAP-fusion/GMAP-fusion/wiki + + diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/fusion.reads_1_2.final --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GMAP/fusion.reads_1_2.final Tue Jul 17 11:52:28 2018 -0400 @@ -0,0 +1,7 @@ +#fusion_name J S trans_acc trans_brkpt geneA chrA coordA geneB chrB coordB junction_type +RPS6KB1--SNF8 10 22 Locus_20_Transcript_1/1_Confidence_1.000_Length_350 156-157 RPS6KB1 chr17 57970686 SNF8 chr17 47021337 ONLY_REF_SPLICE +ACACA--STAC2 9 22 Locus_6_Transcript_1/1_Confidence_1.000_Length_398 170-171 ACACA chr17 35479453 STAC2 chr17 37374426 ONLY_REF_SPLICE +VAPB--IKZF3 1 21 Locus_24_Transcript_1/1_Confidence_1.000_Length_308 168-169 VAPB chr20 56964573 IKZF3 chr17 37934020 ONLY_REF_SPLICE +AHCTF1--NAAA 3 8 Locus_44_Transcript_1/1_Confidence_1.000_Length_339 133-134 AHCTF1 chr1 247094880 NAAA chr4 76846964 ONLY_REF_SPLICE +MED1--ACSF2 4 2 Locus_51_Transcript_1/1_Confidence_1.000_Length_187 88-87 MED1 chr17 37595418 ACSF2 chr17 48548389 ONLY_REF_SPLICE +TOB1--SYNRG 1 1 Locus_26_Transcript_1/1_Confidence_1.000_Length_201 90-91 TOB1 chr17 48943419 SYNRG chr17 35880751 ONLY_REF_SPLICE diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/reads_1.fq.gz Binary file test-data/GMAP/reads_1.fq.gz has changed diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/reads_2.fq.gz Binary file test-data/GMAP/reads_2.fq.gz has changed diff -r 000000000000 -r 966ea55e1aae test-data/GMAP/transcripts.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GMAP/transcripts.fa Tue Jul 17 11:52:28 2018 -0400 @@ -0,0 +1,250 @@ +>Locus_1_Transcript_1/1_Confidence_1.000_Length_106 +GCCATCTTTTACTGCTGTTGGAACACCAGCTACTGTGACTACCCCTGCCAGCAAGCCCAC +TGGCCTGAGCACATGAAGTCCTGCACCCAGTCAGGAGAAGGAGCGC +>Locus_2_Transcript_1/1_Confidence_1.000_Length_1407 +CCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTC +CTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCC +ATAAAAATAAAAAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTT +CATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTCTATTTCCCC +CTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGACTAATCACCACCCAACAAT +GACTAATCAAACTAACCTCAAAACAAATGATAACCATACACAACACTAAAGGACGAACCT +GATCTCTTATACTAGTATCCTTAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCC +TGCCTCACTCATTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCT +TATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCCTAGCCCACT +TCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTAGTTATTATCGAAACCATCA +GCCTACTCATTCAACCAATAGCCCTGGCCGTACGCCTAACCGCTAACATTACTGCAGGCC +ACCTACTCATGCACCTAATTGGAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCT +CTACACTTATCATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCT +TAATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACAACACATAAT +GACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCCCATGACCCCTAACAGGGGC +CCTCTCAGCCCTCCTAATGACCTCCGGCCTAGCCATGTGATTTCACTTCCACTCCATAAC +GCTCCTCATACTAGGCCTACTAACCAACACACTAACCATATACCAATGATGGCGCGATGT +AACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATA +CGGGATAATCCTATTTATTACCTCAGAAATTTTTTTCTTCGCAGGGTTTTTCTGAGCCTT +TTACCACTCCAGCCTAGCCCCTACCCCCCAATTAGGAGGGCACTGGCCCCCAACAGGCAT +CACCCCGCTAAATCCCCTAGAAGTCCCACTCCTAAACACATCCGTATTACTCGCATCAGG +AGTATCAATCACCTGAGCTCACCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCA +AGCACTGCTTATTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTA +CTTCGAGTCTCCCTTCACCATTTCCGA +>Locus_3_Transcript_1/1_Confidence_1.000_Length_351 +TCGCGGGGACACCGGGGGGGCGCCGGGGGCCTCCCACTTATTCTACACCTCTCATGTCTC +TTCACCGTGCCAGACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTGATTCCGCCA +AGCCCGTTCCCTTGGCTGTGGTTTCGCTGGATAGTAGGTAGGGACAGTGGGAATCTCGTT +CATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCA +TAGTTACTCCCGCCGTTTACCCGCGCTTCATTGAATTTCTTCACTTTGACATTCAGAGCA +CTGGGCAGAAATCACATCGCGTCAACACCCGCCGGAGGAGGAGACCCCATT +>Locus_5_Transcript_1/1_Confidence_1.000_Length_226 +TCCGCAAGCCTGTGACGGTCCATTCCCGGGCTCGATGCCGGAAAAACACCTTGGCCCGCC +GGAAGGGCAGGCACATGGGCATAGGTAAGCGGAAGGGTACAGCCAATGCCCGAATGCCAG +AGAAGGTCACATGGATGAGGAGAATGAGGATTTTGCGCCGGCTGCTCAGAAGATACCGTG +AATCTAAGAAGATCGATCGCCACATGTATCACAGCCTGTACCTGAA +>Locus_6_Transcript_1/1_Confidence_1.000_Length_398 +GCTTTTTTGACTATGGATCTTTCTCAGAGATTATGCAGCCCTGGGCACAGACTGTGGTGG +TTGGTAGAGCCAGGCTAGGAGGAATACCTGTGGGAGTTGTTGCTGTAGAAACCCGAACAG +TAGAACTAAGTATCCCAGCTGATCCAGCAAACCTGGATTCTGAAGCCAAGCTCCAGCGAT +TCAAGCGCTCCCTCTCCCTCAAGACCATCCTCCGAAGTAAGAGCTTGGAGAACTTCTTCC +TTCGCTCGGGCTCTGAGCTCAAGTGCCCCACCGAGGTGCTGCTGACGCCCCCAACCCCAC +TGCCCCCTCCCTCCCCACCACCCACAGCCTCGGACAGGGGCCTGGCTACCCCATCCCCCT +CCCCATGCCCAGTCCCACGCCCCCTGGCAGCGCTCAAA +>Locus_7_Transcript_1/2_Confidence_0.667_Length_226 +GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC +GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA +GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC +AAAAAACTGCCCATGTTCTCCGAGTGTGGAGAAAAGAGAGAGAAAG +>Locus_7_Transcript_2/2_Confidence_0.667_Length_268 +GCCCATCGCAGCACCAATGCCCAGGGCAGCCATTGGAAACAGAGGCGGAAATTCCTGCCC +GATGACATTGGCCAGTCACCCATTGTCTCCATGCCGGACGGAGACAAGGTGGACCTGGAA +GCCTTCAGCGAGTTTACCAAGATCATCACCCCGGCCATCACCCGTGTGGTGGACTTTGCC +AAAAAACTGCCCATGTTCTCCGAGCAATTTCGAGTGCAAGTGCCACAGTGTCAGCTAAAG +AAACACAACTGCGGGTTTTCTGCAGAGC +>Locus_8_Transcript_1/1_Confidence_1.000_Length_827 +TGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTTCCTTTTTTGTCTAGATTTT +ATGTATACGGGTTCTTCGAATGTGTGGTAGGGTGGGGGGCATCCATATAGTCACTCCAGG +TTTATGGAGGGTTCTTCTACTATTAGGACTTTTCGCTTCGAAGCGAAGGCTTCTCAAATC +ATGAAAATTATTAATATTACTGCTGTTAGAGAAATGAATGAGCCTACAGATGATAGGATG +TTTCATGTGGTGTATGCATCGGGGTAGTCCGAGTAACGTCGGGGCATTCCGGATAGGCCG +AGAAAGTGTTGTGGGAAGAAAGTTAGATTTACGCCGATGAATATGATAGTGAAATGGATT +TTGGCGTAGGTTTGGTCTAGGGTGTAGCCTGAGAATAGGGGAAATCAGTGAATGAAGCCT +CCTATGATGGCAAATACAGCTCCTATTGATAGGACATAGTGGAAGTGAGCTACAACGTAG +TACGTGTCGTGTAGTACGATGTCTAGTGATGAGTTTGCTAATACAATGCCAGTCAGGCCA +CCTACGGTGAAAAGAAAGATGAATCCTAGGGCTCAGAGCACTGCAGCAGATCATTTCATA +TTGCTTCCGTGGAGTGTGGCGAGTCAGCTAAATACTTTGACGCCGGTGGGGATAGCGATG +ATTATGGTAGCGGAGGTGAAATATGCTCGTGTGTCTACGTCTATTCCTACTGTAAATATA +TGGTGTGCTCACACGATAAACCCTAGGAAGCCAATTGATATCATAGCTCAGACCATACCT +ATGTATCCAAATGGTTCTTTTTTTCCGGAGTAGTAAGTTACAATATG +>Locus_9_Transcript_1/1_Confidence_1.000_Length_131 +TCTAGTCATCCTCGTCGGTCTTCTGCTTCTTGGTATCGACATCGTCATCCTCATCATCTT +CAGCTGCCCGCTTGCCCGTAGCTGACTCAGCTTCCTCATCTTCATCTCCATCCTCTTCCT +CACCACGGCCG +>Locus_10_Transcript_1/1_Confidence_1.000_Length_115 +TGGAATGGGAGACCTGTTGGCCTGTGGGCCTCACCTGCCCCTCTGTTCTCTCCCCTCACA +TCCTCCTGCCCAGCTCCTCACATACCCACACATTCCAGGGCTGGGGTGAGCCTGA +>Locus_11_Transcript_1/1_Confidence_1.000_Length_153 +CCCCCGGTGTCCCCGCGAGGGGCCCGGGGCGGGGTCCGCCGGCCCTGCGGGCCGCCGGTG +AAATACCACTACTCTGATCGTTTTTTCACTGACCCGGTGAGGCGGGGGGGCGAGCCCCGA +GGGGCTCTCGCTTCTGGCGCCAAGCGCCCGGCC +>Locus_12_Transcript_1/1_Confidence_1.000_Length_555 +CCCGGTCGTGTAGCGGTGAAAGTGGTTTGGTTTAGACGTCCGGGAATTGCATCTGTTTTT +AAGCCTAATGTGGGGACAGCTCATGAGTGCAAGACGTCTTGTGATGTAATTATTATACGA +ATGGGGGCTTCAATCGGGAGTACTACTCGATTGTCAACGTCAAGGAGTCGCAGGTCGCCT +GGTTCTAGGAATAATGGGGGAAGTATGTAGGAGTTGAAGATTAGTCCGCCGTAGTCGGTG +TACTCGTAGGTTCAGTACCATTGGTGGCCAATTGATTTGATGGTAAGGGAGGGATCGTTG +ACCTCGTCTGTTATGTAAAGGATGCGTAGGGATGGGAGGGCGATGAGGACTAGGATGATG +GCGGGCAGGATAGTTCAGACGGTTTCCATTTCCTGAGCGTCTGAGATGTTAGTATTAGTT +AGTTTTGTTGTGAGTGTTAGGAAAAGGGCATACAGGACTAGGAAGCAGATAAGGAAAATG +ATTATGAGGGCGTGATCATGAAAGGTGATAAGCTCTTCTATGATAGGGGAAGTAGCGTCT +TGTAGACCTACTTGC +>Locus_13_Transcript_1/1_Confidence_1.000_Length_306 +GCCGGAGTAGTAAGTTACAATATGGGAGATTATTCCGAAGCCTGGTAGGATAAGAATATA +AACTTCAGGGTGACCGAAAAATCAGAATAGGTGTTGGTATAGAATGGGGTCTCCTCCTCC +GGCGGGGTCGAAGAAGGTGGTGTTGAGGTTGCGGTCTGTTAGTAGTATAGTGATGCCAGC +AGCTAGGACTGGGAGAGATAGGAGAAGTAGGACTGCTGTGATTAGGACGGATCAGACGAA +GAGGGGCGTTTGGTATTGGGTTATGGCAGGGGGTTTTATATTGATAATTGTTGTGATGAA +ATTGAT +>Locus_14_Transcript_1/1_Confidence_1.000_Length_171 +GGCCACCAGGCGTTTAACCGACGCTTTCTTGTTGTTGCGGAATAATTCCATCCAAAACCG +GCAGCTGTTAGCCGAGCAAGTTCAAAATGAGCCTGTTTGGAACAACCTCAGGTTTTGGAA +CCAGTGGGACCAGCATGTTTGGCAGTGCAACTACAGACAATCACAATCCCA +>Locus_16_Transcript_1/1_Confidence_1.000_Length_109 +AGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAG +GTAGCATAATCACTTGTTCCTTAAATAGGGCCCTGTATGAATGGCTCCA +>Locus_17_Transcript_1/1_Confidence_1.000_Length_138 +GACCTGCTAGGGTGAGAAGGATTATTCGAGTGCTATAGGCGCTTGTCAGGGAGGTAGCGA +TGAGAGTAATAGATAGGGCTCAGGCGTTTGTGTATGATATGTTTGCGGTTTCGATGATGT +GGTCTTTGGAGTAGAAAC +>Locus_19_Transcript_1/1_Confidence_1.000_Length_232 +CTAACCGGCTTTTTGCCCAAATGAGCCATTATCGAAGAATTCACAAAAAACAATAGCCTC +ATCATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACCTACGCCTA +ATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAACGTAAAAATAAAATGACAG +TTTGAACATACAAAACCCACCCCATTCCTCCCCACACTCATCGCCCTTACCA +>Locus_20_Transcript_1/1_Confidence_1.000_Length_350 +GGCGGGTCCGGGCCCATGAGGCGACGAAGGAGGCGGGACGGCTTTTACCCAGCCCCGGAC +TTCCGAGACAGGGAAGCTGAGGACATGGCAGGAGTGTTTGACATAGACCTGGACCAGCCA +GAGGACGCGGGCTCTGAGGATGAGCTGGAGGAGGGGGCCAAGTATAAGGAGCGAGGGACG +GTCTTGGCTGAGGACCAGCTAGCCCAGATGTCAAAGCAGTTGGACATGTTCAAGACCAAC +CTGGAGGAATTTGCCAGCAAACACAAGCAGGAGATCCGGAAGAATCCTGAGTTCCGTGTG +CAGTTCCAGGACATGTGTGCAACCATTGGCGTGGATCCGCTGGCCTCTGG +>Locus_21_Transcript_1/2_Confidence_0.667_Length_119 +TGTAGATCCAAGTGTGGAAGGCTGACCTTGCATCCATGGCAACCATAAAGTAGGGTCCAT +GACTCTTCTCTCCCTTTCTCTCTCTTTTCTCCACACTCGGAGAACATGGGCAGTTTTTT +>Locus_21_Transcript_2/2_Confidence_0.667_Length_222 +TGTAGATCCAAGTGTGGAAGGCTGACCTTGCATCCATGGCAACCATAAAGTAGGGTCCAT +GACTCTTCTCTCCCTTTCTCTCTCTTTTCTCCACACTTTGAAAGGAGGATGTGTGGACCC +TTTCTCCTATATGCTTATGTCTCTGTTGTCGTAGATTGGCGTCCTTTGTGAGCTATTCAG +TGACATTTCAGAACCATTTTGCTCTGCAGAAAACCCGCAGTT +>Locus_22_Transcript_1/1_Confidence_1.000_Length_302 +GGTTGTTGATGAGATATTTGGAGGAGGCCTAGTAGTGGGGTGAGGCTTGGATTAGCGTTT +AGAAGGGCTATTTGTTGTGGGTCTCATGAGTTGGAGTGTAGGATAAATCATGCTAAGGCG +AGGATGAAACCGATATCGCCGATACGGTTGTATAGGATTGCTTGAATGGCTGCTGTGTTG +GCATCTGCTCGGGCGTATCATCAACTGATGAGCAAGAAGGATATAATTCCTACGCCCTCT +CAGCCGATGAACAGTTGGAATAGGTTGTTAGCGGTAACTAAGATTAGTATGGTAATTAGG +AA +>Locus_24_Transcript_1/1_Confidence_1.000_Length_308 +GACCGGTCCCCGCCTTTTTGTAAAACTTAAAGCGGGCGCAGCATTAACGCTTCCCGCCCC +GGTGACCTCTCAGGGGTCTCCCCGCCAAAGGTGCTCCGCCGCTAAGGAACATGGCGAAGG +TGGAGCAGGTCCTGAGCCTCGAGCCGCAGCACGAGCTCAAATTCCGAGCAAGTGCGGAGG +CAAGACACATCAAAGCAGAGATGGGAAGTGAAAGAGCTCTCGTACTGGACAGATTAGCAA +GCAATGTGGCAAAACGAAAAAGCTCAATGCCTCAGAAATTCATTGGTGAGAAGCGCCACT +GCTTTGAT +>Locus_25_Transcript_1/1_Confidence_1.000_Length_101 +CATGATCCTGCAATAAGAAAGTTCCCCGGCAAGGTTGGTGGGCTAAAAGACAGACAACCA +ATGCTATCATCAGGAGATGATGTTACTTCAATATCCTTCAT +>Locus_26_Transcript_1/1_Confidence_1.000_Length_201 +CGCCGCTCCCGACCCTCCCGCGCCCCCGCCCTGCCGCGCTGCTCCCCGCCCAGCCGCGGG +TCTGTGGTCCAAGCCGCCCCGAAGCAGCCCCCAGATGAAAACTCGCTGGATTTTTCCTCC +TGTATGTTACGGCCTGGGATTAAAAATGCTCAGGAGCTTGCCTGTGGAGTGTGCCTCTTG +AATGTGGACTCGAGGAGCCGG +>Locus_27_Transcript_1/1_Confidence_1.000_Length_421 +TAAGATTTGCCGAGTTCCTTTTACTTTTTTTAACCTTTCCTTATGAGCATGCCTGTGTTG +GGTTGACAGTGAGGGTAATAATGACTTGTTGGTTGATTGTAGATATTGGGCTGTTAATTG +TCAGTTCAGTGTTTTAATCTGACGCAGGCTTATGCGGAGGAGAATGTTTTCATGTTACTT +ATACTAACATTAGTTCTTCTATAGGGTGATAGATTGGTCCAATTGGGTGTGAGGAGTTCA +GTTATATGTTTGGGATTTTTTAGGTAGTGGGTGTTGAGCTTGAACGCTTTCTTAATTGGT +GGCTGCTTTTAGGCCTACTATGGGTGTTAAATTTTTTACTCTCTCTACAAGGTTTTTTCC +TAGTGTCCAAAGAGCTGTTCCTCTTTGGACTAACAGTTAAATTTACAAGTGGATTTAGAG +G +>Locus_28_Transcript_1/1_Confidence_1.000_Length_343 +AGAGAGGGAGGTAAGAGTCAGAAGCTTATGTTGTTTATGCGGGGAAACGCCATATCGGGG +GCACCGATTATTAGGGGAACTAGTCAGTTGCCAAAGCCTCCGATTATGATGGGTATTACT +ATGAAGAAGATTATTACAAATGCATGGGCTGTGACGATAACGTTGTAGATGTGGTCGTTA +CCTAGAAGGTTGCCTGGCTGGCCCAGCTCGGCTCGAATAAGGAGGCTTAGAGCTGTGCCT +AGGACTCCAGCTCATGCGCCGAATAATAGGTATAGTGTTCCAATGTCTTTGTGGTTTGTA +GAGAATAGTCAACGGTCGGCGAACATCAGTGGGGGTGAGGTAA +>Locus_29_Transcript_1/1_Confidence_1.000_Length_119 +GAGATGATATACAGGTTTTTGGCTCCTGTGTTGTCAGCACAATTGATTACAGCTCCTACC +GGAAGACCCAAGGAAATCCGGAATTTCGCACCAGAGGACCCACCACGTCCTCGCTTCGA +>Locus_32_Transcript_1/1_Confidence_1.000_Length_180 +CGGCCGCAGCCATGAGTATGCTCAGGCTTCAGAAGAGGCTCGCCTCTAGTGTCCTCCGCT +GTGGCAAGAAGAAGGTCTGGTTAGACCCCAATGAGACCAATGAAATCGCCAATGCCAACT +CCCGTCAGCAGATCCGGAAGCTCATCAAAGATGGGCTGATCATCCGCAAGCCTGTGACGG +>Locus_33_Transcript_1/1_Confidence_1.000_Length_127 +ACTCCTGCTCGCATCTGCTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCC +TCCCTTAGCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTCCTT +ACACCTA +>Locus_35_Transcript_1/1_Confidence_1.000_Length_307 +CCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCT +CATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAA +ACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCT +AACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGG +ATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACCACAAGGCA +CACCTAC +>Locus_36_Transcript_1/1_Confidence_1.000_Length_246 +CTTGTTTTATTTTAATGGCTGATCTATGTAATCACAGAGGCCAGTATGTACAGACAAAGT +GGGAGGTTTTATTTCTTGGTCTCTTCCTCCTTGGATAAAGTCTTGATGATCTCCTCCTTC +TTGGCCTGGAGGCGCTCTTCACGGCGCTTGCGTGCTTCCTTGGTCTTAGACCTGCGGGCC +TCAGCCTGGTCAGCCAGGAGCTTCTTGCGGGCCTTGTCTGCCTTCAGCTTGTGGATGTGT +TCCATG +>Locus_37_Transcript_1/1_Confidence_1.000_Length_172 +TCTCACTGTGGGTTCTGAGGAAACTCTCAGGGGAAGACAGCTCTTCATACCCTCACATAA +CCCCACCCACACACAGGCCCAGAGACACCTACAGACACACCCCCGCCCCATCTCTCACAC +TCACACTCACACACTTGCGTGTCAGACACCTGCAGACATACATGCTCCTGCC +>Locus_38_Transcript_1/1_Confidence_1.000_Length_212 +ACGGGATGGATCCAGGATGTAGTCTGTGTTACATGATTGATGAAGTACTTGATTCCATCT +GCTGTGTAAGCTTCCTCCCACCCATAAGGTAAACCCTCGGTTTCCCCCTGAGCTTTCATC +CTGAAGGCGAGGAGAAGCTAGATCCGCCACAAAAGGATAAGCCCTTCCCCACCACTAACG +GAGGAAACAAGTTGGCTCGGGATCCCGGGACG +>Locus_40_Transcript_1/1_Confidence_1.000_Length_132 +CCCTGGGCAATGACGTCTTCAATGTTTTTTCCATTCAGCTCACTGATAACCTTGTTGAGC +CGGTCGTCGTCCGCCTCGATACCCACGCTGTCCAAGATCTTCTTGATGTCCTTGGCGCTG +GGGGAGGAGTTG +>Locus_41_Transcript_1/1_Confidence_1.000_Length_194 +TAGGATCCTCTACGCACAACGCCTGCTCGCCTCCTCCGTGTGGTTGCCAAGCCAAGCCGC +CTGCTACCTTCATCACCAAATTGCACTCGCTCCTTCCTGGAATCCTTTTTCCTAGCTTCA +CCACCAAATCGTTAGCGCTCCTTCCTTCTTCCTAGCTTCCTTCACCAAATCGCACTGGCT +CCTGGACTCTTTTC +>Locus_43_Transcript_1/1_Confidence_1.000_Length_109 +TGGAATTAAGGGTGTTAGTCATGTTAGCTTGTTTCAGGTGCGAGATAGTAGTAGGGTCGT +GGTGCTGGAGTTTAAGTTGAGTAGTAGGAATGCGGTAGTAGTTAGGATA +>Locus_44_Transcript_1/1_Confidence_1.000_Length_339 +GGGTGTGAGCCCGGCCCGTGGCGGCCACGTCTCCCGGGAGATGCTGTGACGGACCCGCAC +GGGAGGAGCTCGCGCCTGGCCTGGCGACCCGGTGGACTCGGCCCGCGGCGGCGCGCTCAC +CCGCCCCGTTCAGATAAAGGCTGGTGGTGGGAGAATGCTATCGCTGCCCTGTTTCGGAGA +CACATTCCCGTCAGCTGGCTGATCCGCGCTACCCTGAGTGAGTCGGAAAACTTCGAAGCA +GCTGTTGGCAAGTTGGCCAAGACTCCCCTTATTGCTGATGTTTATTACATTGTTGGTGGC +ACGTCCCCCCGGGAGGGGGTGGTCATCACGAGGAACAGA +>Locus_45_Transcript_1/1_Confidence_1.000_Length_121 +AGACCCTATGGAGCTTTAATTTATTAATGCAAGCAGTACCTAACAAACCCACAGGTCCTA +AACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTC +C +>Locus_46_Transcript_1/1_Confidence_1.000_Length_122 +GGTCTTCTCGTCTTGCTGTGTCATGCCCGCCTCTTCACGGGCAGGTCAATTTCACTGGTT +AAAAGTAAGAGACAGCTGAACCCTCGTGGAGCCATTCATACAGGTCCCTATTTAAGGAAC +AA +>Locus_47_Transcript_1/1_Confidence_1.000_Length_156 +GGGCACTCTCTGCCTGGGTCCGTTCTTCTTCCCTCTGGGCCTGGATGGCCTCCATTTCTG +TCTGCTGCTCCTTTAGCCTCATTTCCAGCTCCATTTTTTCCCTTTCTAAGCTCTCCAGAG +CCTTTGCCAGCTCCTGCTGGTGCCAGGAGCGCTCCT +>Locus_48_Transcript_1/1_Confidence_1.000_Length_185 +GTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCT +ATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGAC +CCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAA +AATAG +>Locus_50_Transcript_1/1_Confidence_1.000_Length_125 +TCCGAACCCCCTCATGATTCTCGATTTTGCTGATAATCTTGATGTTCTTTCCCTTCTCTC +CCAGGACCTTCCTAACTTCATGGACATCAGATGCCTTGCGGATGAATGACGCAAACACCA +TATCA +>Locus_51_Transcript_1/1_Confidence_1.000_Length_187 +GTCCACGCTTTCTGCCTTCTGCTCCACAGTGTCCTCAGGGAAGTGCGCGAATGTCACGGG +ACTGTTCTCTGTGGTTCCATAAGCAACCTTAGCTGCTGTACAAGCTCCGGACAGCTCACA +GGATTCTCCCCATGGTGAGCCACTTTTACATCACAAAGCTGTCCTGCAGGATCTAACTGC +ACTTCCA diff -r 000000000000 -r 966ea55e1aae tool-data/ctat_genome_resource_libs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/ctat_genome_resource_libs.loc.sample Tue Jul 17 11:52:28 2018 -0400 @@ -0,0 +1,15 @@ +# This file lists the locations of CTAT Genome Resource Libraries +# Usually there will only be one library, but it is concievable +# that there could be multiple libraries. +# This file format is as follows +# (white space characters are TAB characters): +# +# +# value is a unique id +# name is the display name +# path is the directory where the genome resource lib files are stored +# +#ctat_genome_resource_libs.loc could look like: +# +#GRCh38_v27_CTAT_lib_Feb092018 CTAT_GenomeResourceLib_GRCh38_v27_CTAT_lib_Feb092018 /path/to/ctat/genome/resource/lib/directory +# diff -r 000000000000 -r 966ea55e1aae tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Jul 17 11:52:28 2018 -0400 @@ -0,0 +1,14 @@ + + + value, name, path + +
+ + value, name, path + +
+ + value, name, path + +
+